Contacts of the helix formed by residues 504 - 514 (chain D) in PDB entry 1M7X
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with HIS 504 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492D TYR* 4.4 8.1 - - - -
500D ARG 3.4 5.8 + - - +
501D GLN 4.3 3.1 - - - +
502D TYR 3.7 1.0 - - - -
503D HIS* 1.3 76.5 - - - +
505D ASP* 1.3 56.5 + - - +
507D LEU* 3.2 20.4 + - - +
508D THR* 3.3 22.3 + - + +
631D VAL 3.0 33.7 + - - -
632D ASP* 4.2 2.5 - - - -
633D ASP 3.4 18.5 + - - -
634D LYS* 3.5 49.2 + - + +
637D SER* 4.3 10.5 - - - -
638D VAL 4.2 0.4 + - - -
639D LEU* 3.4 38.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 505 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502D TYR 4.5 2.8 - - - +
503D HIS* 3.6 17.0 + - - +
504D HIS* 1.3 75.3 + - - +
506D LYS* 1.3 66.1 + - - +
507D LEU 2.9 5.6 - - - -
508D THR* 3.3 13.9 - - - +
509D PHE* 2.9 42.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 506 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488D ASP* 3.3 57.8 + - + +
489D THR* 3.9 7.1 + - - +
491D ASP* 3.9 21.9 + - + +
492D TYR* 3.8 20.2 - - + +
495D LEU* 4.5 4.7 - - + -
503D HIS* 3.0 47.8 + - + +
505D ASP* 1.3 84.2 - - - +
507D LEU* 1.3 64.5 + - - +
509D PHE* 4.7 2.1 + - - +
510D GLY 5.3 2.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 507 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485D TRP* 5.9 0.5 + - - -
489D THR* 3.8 27.3 - - + +
492D TYR* 3.3 57.9 - - + +
493D MET* 5.7 0.9 - - - -
504D HIS* 3.2 10.7 + - + +
505D ASP 2.9 0.4 - - - -
506D LYS* 1.3 81.1 - - - +
508D THR* 1.3 61.3 + - - +
509D PHE 3.5 0.9 - - - -
510D GLY 4.2 3.7 + - - -
553D TYR* 6.4 0.7 - - + -
556D TRP* 3.6 34.5 + - + +
560D PHE* 3.9 12.5 - - - -
639D LEU* 3.8 18.6 - - + -
657D PHE* 3.5 26.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 508 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504D HIS* 3.3 30.0 + - - +
505D ASP* 3.3 18.0 - - - +
507D LEU* 1.3 72.8 - - - +
509D PHE* 1.3 67.4 + - - +
510D GLY 3.3 3.3 + - - -
511D ILE* 3.4 19.1 + - - +
512D LEU* 4.3 5.4 + - - +
628D TRP* 3.6 18.2 + - + -
631D VAL* 3.7 25.6 - - + +
639D LEU* 3.8 14.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 509 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488D ASP* 4.1 17.5 - - - +
505D ASP* 2.9 27.2 + - + +
506D LYS* 5.1 2.2 - - - -
507D LEU 3.5 0.2 - - - -
508D THR* 1.3 78.0 + - - +
510D GLY* 1.3 67.5 + - - +
512D LEU* 2.9 44.7 + - + +
513D TYR* 3.2 44.1 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 510 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482D ASN* 5.4 2.1 + - - -
485D TRP* 4.9 7.2 - - - -
488D ASP* 5.7 0.8 + - - -
506D LYS 5.3 2.2 + - - -
507D LEU 4.2 4.8 + - - -
508D THR 3.3 2.0 - - - -
509D PHE* 1.3 77.9 - - - +
511D ILE* 1.3 61.2 + - - +
513D TYR* 3.4 23.8 + - - -
514D ASN* 3.2 21.0 + - - +
560D PHE* 3.7 23.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 511 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
508D THR 3.4 6.3 + - - +
509D PHE 3.0 1.0 + - - -
510D GLY* 1.3 76.0 - - - +
512D LEU* 1.3 68.7 + - + +
513D TYR 3.1 1.2 + - - -
514D ASN* 3.3 16.4 + - + +
515D TYR* 3.9 21.8 - - + +
560D PHE* 3.5 24.0 - - + -
561D PRO* 4.0 14.1 - - + -
626D PHE* 3.4 56.5 - - + -
628D TRP* 3.7 22.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 512 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
508D THR 4.4 4.7 - - - +
509D PHE* 2.9 47.0 + - + +
511D ILE* 1.3 84.1 - - + +
513D TYR* 1.3 56.9 + - + +
515D TYR* 5.2 2.7 + - - +
516D THR* 5.2 2.1 - - - +
628D TRP* 6.0 2.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 513 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482D ASN* 3.0 36.0 + - - -
484D GLY* 3.7 7.6 - - - -
485D TRP* 3.2 20.3 + - - +
488D ASP* 4.5 2.1 + - - -
509D PHE* 3.2 53.4 - + + -
510D GLY* 3.9 11.9 - - - -
511D ILE 3.2 0.4 - - - -
512D LEU* 1.3 76.7 - - + +
514D ASN* 1.3 58.1 + - - +
515D TYR 2.9 10.8 + - - -
516D THR* 2.5 42.2 + - + +
519D PHE* 3.5 22.5 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 514 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482D ASN* 5.6 2.2 - - - +
510D GLY 3.2 17.4 + - - +
511D ILE* 3.3 17.7 + - + +
513D TYR* 1.3 76.8 - - - +
515D TYR* 1.3 73.2 + - + +
516D THR 3.5 0.4 - - - -
517D GLU 3.2 16.9 - - - +
519D PHE* 4.0 17.1 - - - +
560D PHE* 4.8 4.4 - - - -
561D PRO* 3.1 42.9 + - - +
562D GLY* 4.3 2.2 - - - +
620D ASP 3.0 20.4 + - - +
621D PHE* 4.7 8.1 - - - -
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il